Trouble with baking cylindrical objects
Will this old method work for you ... using a prerendered hemisphere normal texture.

Basically I have attached a shadeless material of a normal rendering of a hemisphere. You will find the image packed in the blend file. Using a orthographic camera I render from the top view of the model. Also I have replaced the color of the background to a flat normal color which is (R0.5,G0.5,B1.0)



This is where you change the background color under the world tab on the
properties panel.



Hit the render button on the Render panel and you should get this result.





Let me know if you have further queries.